That kind of clashes with Hyperion's claim, and this is where the whole thing crumbles.

Also if Cloanto have rights to Workbench and Kickstart and code, what are they doing going around enforcing the Amiga brand, taking down videos on Youtube, etc?

Even if we agree, from the little evidence we have, that Hyperion and Cloanto share somehow rights to the operating system and its parts, and a license to sell it and modify it, it is still unsure who, if any, owns the brand and trademarks related to Amiga as a whole, and from the information being available to us throughout the years, it is not clear or any way implied to me that either of these companies own that, having instead just a license to use the names and trademarks in relation to the licenses they may have (ie name of the OS, use for related promotion etc).

So why does an A1200 case project, just to name one example. have to seek permission to use the Amiga trademark and name? And who did they get this permission from? This is very important, especially if any money has passed through hands, because it's potentially illegal (for whoever "granted" the permission). And even if there was no monetary exchange, who can give permission to use something they don't own to someone else??

Both Hyperion and Cloanto own pieces of the code. Cloanto pre-1993, Hyperion thereafter. The case is simple, Amiga Inc does own the trademarks. This is well documented by the European trademark office for example.